HEADER OXIDOREDUCTASE 02-DEC-15 5FPL
TITLE CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH CCT363901
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE
COMPND 3 5B;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: JMJC DOMAIN, RESIDUES 25-101,374-772;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE
KEYWDS OXIDOREDUCTASE, LYSINE-SPECIFIC DEMETHYLASE 5B
EXPDTA X-RAY DIFFRACTION
AUTHOR V.SRIKANNATHASAN,L.B.YANN-VAI,R.NOWAK,C.JOHANSSON,C.GILEADI,F.VON
AUTHOR 2 DELFT,C.H.ARROWSMITH,C.BOUNTRA,A.EDWARDS,P.BRENNAN,K.HUBER,
AUTHOR 3 U.OPPERMANN
REVDAT 6 20-NOV-24 5FPL 1 REMARK
REVDAT 5 10-JAN-24 5FPL 1 REMARK LINK
REVDAT 4 24-JAN-18 5FPL 1 JRNL
REVDAT 3 14-DEC-16 5FPL 1 AUTHOR
REVDAT 2 09-MAR-16 5FPL 1 JRNL
REVDAT 1 20-JAN-16 5FPL 0
JRNL AUTH V.BAVETSIAS,R.M.LANIGAN,G.F.RUDA,B.ATRASH,M.G.MCLAUGHLIN,
JRNL AUTH 2 A.TUMBER,N.Y.MOK,Y.LE BIHAN,S.DEMPSTER,K.J.BOXALL,
JRNL AUTH 3 F.JEGANATHAN,S.B.HATCH,P.SAVITSKY,S.VELUPILLAI,T.KROJER,
JRNL AUTH 4 K.S.ENGLAND,J.SEJBERG,C.THAI,A.DONOVAN,A.PAL,G.SCOZZAFAVA,
JRNL AUTH 5 J.M.BENNETT,A.KAWAMURA,C.JOHANSSON,A.SZYKOWSKA,C.GILEADI,
JRNL AUTH 6 N.A.BURGESS-BROWN,F.VON DELFT,U.OPPERMANN,Z.WALTERS,
JRNL AUTH 7 J.SHIPLEY,F.I.RAYNAUD,S.M.WESTAWAY,R.K.PRINJHA,O.FEDOROV,
JRNL AUTH 8 R.BURKE,C.J.SCHOFIELD,I.M.WESTWOOD,C.BOUNTRA,S.MULLER,
JRNL AUTH 9 R.L.M.VAN MONTFORT,P.E.BRENNAN,J.BLAGG
JRNL TITL 8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONE DERIVATIVES
JRNL TITL 2 AS POTENT, CELL PERMEABLE, KDM4 (JMJD2) AND KDM5 (JARID1)
JRNL TITL 3 HISTONE LYSINE DEMETHYLASE INHIBITORS.
JRNL REF J.MED.CHEM. V. 59 1388 2016
JRNL REFN ISSN 0022-2623
JRNL PMID 26741168
JRNL DOI 10.1021/ACS.JMEDCHEM.5B01635
REMARK 2
REMARK 2 RESOLUTION. 2.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.10.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.17
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 38565
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 1949
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 19
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.41
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2957
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2414
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2814
REMARK 3 BIN R VALUE (WORKING SET) : 0.2393
REMARK 3 BIN FREE R VALUE : 0.2839
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.84
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3644
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 34
REMARK 3 SOLVENT ATOMS : 279
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 65.42
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.20
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.04030
REMARK 3 B22 (A**2) : 0.04030
REMARK 3 B33 (A**2) : -0.08070
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.286
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.203
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.162
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.190
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.158
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 3881 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 5289 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1298 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 89 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 588 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 3881 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 3 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 486 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 9 ; 1.000 ; HARMONIC
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 4494 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.07
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.25
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.79
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: {A|25 - 375}
REMARK 3 ORIGIN FOR THE GROUP (A): 87.7146 70.9559 17.8285
REMARK 3 T TENSOR
REMARK 3 T11: -0.2428 T22: 0.1637
REMARK 3 T33: -0.1092 T12: -0.1880
REMARK 3 T13: 0.0198 T23: -0.0692
REMARK 3 L TENSOR
REMARK 3 L11: 2.5556 L22: 1.4576
REMARK 3 L33: 3.0510 L12: 0.2162
REMARK 3 L13: -0.1350 L23: -0.2293
REMARK 3 S TENSOR
REMARK 3 S11: 0.0580 S12: -0.2087 S13: 0.1129
REMARK 3 S21: 0.0106 S22: -0.1624 S23: -0.0173
REMARK 3 S31: 0.1464 S32: -0.2742 S33: 0.1044
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: {A|376 - 594}
REMARK 3 ORIGIN FOR THE GROUP (A): 88.1217 66.3227 13.9997
REMARK 3 T TENSOR
REMARK 3 T11: -0.2251 T22: 0.1493
REMARK 3 T33: -0.1377 T12: -0.1832
REMARK 3 T13: 0.0516 T23: -0.0342
REMARK 3 L TENSOR
REMARK 3 L11: 1.9647 L22: 1.0033
REMARK 3 L33: 2.6633 L12: -0.0677
REMARK 3 L13: 0.4017 L23: -0.3590
REMARK 3 S TENSOR
REMARK 3 S11: 0.0089 S12: -0.0605 S13: 0.0009
REMARK 3 S21: -0.0595 S22: -0.0528 S23: 0.0058
REMARK 3 S31: 0.3528 S32: -0.3647 S33: 0.0439
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: {A|595 - 754}
REMARK 3 ORIGIN FOR THE GROUP (A): 57.4338 64.6960 6.2049
REMARK 3 T TENSOR
REMARK 3 T11: -0.2178 T22: 0.1522
REMARK 3 T33: -0.0594 T12: -0.0164
REMARK 3 T13: 0.0033 T23: -0.0586
REMARK 3 L TENSOR
REMARK 3 L11: 2.7385 L22: 0.6363
REMARK 3 L33: 1.2273 L12: 0.5237
REMARK 3 L13: 0.5532 L23: -0.7238
REMARK 3 S TENSOR
REMARK 3 S11: -0.1331 S12: 0.4321 S13: 0.1541
REMARK 3 S21: -0.1481 S22: 0.2486 S23: 0.1400
REMARK 3 S31: -0.1250 S32: 0.2229 S33: -0.1155
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5FPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-15.
REMARK 100 THE DEPOSITION ID IS D_1290065692.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-JUL-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : M
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38565
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350
REMARK 200 RESOLUTION RANGE LOW (A) : 46.170
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 20.10
REMARK 200 R MERGE (I) : 0.15000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 19.70
REMARK 200 R MERGE FOR SHELL (I) : 0.15000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 14.27
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 5A1F
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 69.65
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 0.8M POTASSIUM
REMARK 280 PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.40000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.70000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.05000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.35000
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.75000
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.40000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 50.70000
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.35000
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 76.05000
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.75000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 LEU A 101
REMARK 465 GLY A 102
REMARK 465 GLY A 103
REMARK 465 GLY A 104
REMARK 465 GLY A 105
REMARK 465 LYS A 444
REMARK 465 TYR A 755
REMARK 465 ASN A 756
REMARK 465 GLU A 757
REMARK 465 TRP A 758
REMARK 465 ALA A 759
REMARK 465 LEU A 760
REMARK 465 ASN A 761
REMARK 465 VAL A 762
REMARK 465 ASN A 763
REMARK 465 GLU A 764
REMARK 465 ALA A 765
REMARK 465 LEU A 766
REMARK 465 GLU A 767
REMARK 465 ALA A 768
REMARK 465 LYS A 769
REMARK 465 ILE A 770
REMARK 465 ASN A 771
REMARK 465 LYS A 772
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 40 CG CD OE1 OE2
REMARK 470 LYS A 51 CD CE NZ
REMARK 470 LYS A 100 NZ
REMARK 470 LYS A 408 CE NZ
REMARK 470 SER A 431 OG
REMARK 470 LYS A 432 CD CE NZ
REMARK 470 GLU A 433 CG CD OE1 OE2
REMARK 470 LYS A 446 NZ
REMARK 470 ASP A 478 CG OD1 OD2
REMARK 470 LYS A 483 CD CE NZ
REMARK 470 LYS A 535 CD CE NZ
REMARK 470 LYS A 536 CD CE NZ
REMARK 470 LYS A 540 CE NZ
REMARK 470 SER A 544 OG
REMARK 470 LEU A 548 CD1
REMARK 470 LEU A 549 CG CD1 CD2
REMARK 470 LEU A 620 CD1 CD2
REMARK 470 LYS A 639 NZ
REMARK 470 LYS A 653 CE NZ
REMARK 470 LYS A 671 NZ
REMARK 470 LYS A 694 NZ
REMARK 470 LYS A 709 CE NZ
REMARK 470 LYS A 720 CG CD CE NZ
REMARK 470 GLU A 753 CD OE1 OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 ND1 HIS A 399 O HOH A 2085 2.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASP A 420 53.16 -112.02
REMARK 500 PHE A 493 -3.28 77.83
REMARK 500 ALA A 538 71.56 -151.82
REMARK 500 PHE A 700 -58.96 -135.67
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2102 DISTANCE = 6.34 ANGSTROMS
REMARK 525 HOH A2131 DISTANCE = 5.91 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 801 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 413 O
REMARK 620 2 THR A 416 O 84.5
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 802 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 499 NE2
REMARK 620 2 GLU A 501 OE2 93.4
REMARK 620 3 HIS A 587 NE2 83.5 79.3
REMARK 620 4 QAY A 901 N2 84.5 101.3 168.0
REMARK 620 5 QAY A 901 N1 81.6 128.3 149.2 27.2
REMARK 620 6 QAY A 901 N5 97.7 168.9 102.1 79.7 53.8
REMARK 620 7 HOH A2141 O 167.5 83.4 84.1 107.9 109.9 85.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 800 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 692 SG
REMARK 620 2 CYS A 695 SG 106.3
REMARK 620 3 CYS A 715 SG 118.1 110.7
REMARK 620 4 HIS A 718 ND1 112.4 111.0 98.4
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 800
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QAY A 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1755
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1756
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1757
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5FPU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH GSKJ1
REMARK 900 RELATED ID: 5FPV RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND KDOAM20A
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUE NUMBER 0-MET FROM THE CONSTRUCT. KDM5B START WITH
REMARK 999 PHE26. GGGG (101-105) FOUR GLYCINE LINKER INTRODUCED BUT
REMARK 999 NO DENSITY OBSERVED FOR THESE RESIDUES.
DBREF 5FPL A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101
DBREF 5FPL A 374 772 UNP Q9UGL1 KDM5B_HUMAN 374 772
SEQADV 5FPL MET A 0 UNP Q9UGL1 EXPRESSION TAG
SEQADV 5FPL GLY A 102 UNP Q9UGL1 LINKER
SEQADV 5FPL GLY A 103 UNP Q9UGL1 LINKER
SEQADV 5FPL GLY A 104 UNP Q9UGL1 LINKER
SEQADV 5FPL GLY A 105 UNP Q9UGL1 LINKER
SEQRES 1 A 480 MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO
SEQRES 2 A 480 SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE HIS
SEQRES 3 A 480 LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS LYS
SEQRES 4 A 480 VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA CYS
SEQRES 5 A 480 ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN ARG
SEQRES 6 A 480 LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU GLY
SEQRES 7 A 480 GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE GLY
SEQRES 8 A 480 GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN MET
SEQRES 9 A 480 PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS GLU
SEQRES 10 A 480 PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL THR
SEQRES 11 A 480 VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE GLY
SEQRES 12 A 480 SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SER
SEQRES 13 A 480 PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN LEU
SEQRES 14 A 480 ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA HIS
SEQRES 15 A 480 ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP LEU
SEQRES 16 A 480 TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS ILE
SEQRES 17 A 480 GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS TRP
SEQRES 18 A 480 GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR ALA
SEQRES 19 A 480 ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA PRO
SEQRES 20 A 480 LYS LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN LEU
SEQRES 21 A 480 VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS GLU
SEQRES 22 A 480 VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU PHE
SEQRES 23 A 480 VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE ASN
SEQRES 24 A 480 GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS THR
SEQRES 25 A 480 VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU HIS
SEQRES 26 A 480 TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS ASP
SEQRES 27 A 480 GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL LEU
SEQRES 28 A 480 ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET ALA
SEQRES 29 A 480 ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR VAL
SEQRES 30 A 480 ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP PHE
SEQRES 31 A 480 GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS CYS
SEQRES 32 A 480 LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER CYS
SEQRES 33 A 480 LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS GLU
SEQRES 34 A 480 LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG TYR
SEQRES 35 A 480 ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN ALA
SEQRES 36 A 480 LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA LEU
SEQRES 37 A 480 ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE ASN LYS
HET ZN A 800 1
HET MN A 801 1
HET MN A 802 1
HET QAY A 901 19
HET EDO A1755 4
HET EDO A1756 4
HET DMS A1757 4
HETNAM ZN ZINC ION
HETNAM MN MANGANESE (II) ION
HETNAM QAY 8-[4-(2-AZANYLETHYL)PYRAZOL-1-YL]-3H-PYRIDO[3,4-
HETNAM 2 QAY D]PYRIMIDIN-4-ONE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM DMS DIMETHYL SULFOXIDE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN ZN 2+
FORMUL 3 MN 2(MN 2+)
FORMUL 5 QAY C12 H12 N6 O
FORMUL 6 EDO 2(C2 H6 O2)
FORMUL 8 DMS C2 H6 O S
FORMUL 9 HOH *279(H2 O)
HELIX 1 1 SER A 38 ALA A 43 1 6
HELIX 2 2 ASP A 44 GLU A 57 1 14
HELIX 3 3 LEU A 379 ASN A 395 1 17
HELIX 4 4 PRO A 397 VAL A 401 5 5
HELIX 5 5 PRO A 402 THR A 416 1 15
HELIX 6 6 SER A 431 GLY A 435 1 5
HELIX 7 7 SER A 448 TYR A 454 1 7
HELIX 8 8 ASN A 463 MET A 467 5 5
HELIX 9 9 VAL A 471 ILE A 475 5 5
HELIX 10 10 ILE A 479 LEU A 484 1 6
HELIX 11 11 GLU A 501 SER A 505 5 5
HELIX 12 12 PRO A 523 TYR A 525 5 3
HELIX 13 13 ALA A 526 ALA A 538 1 13
HELIX 14 14 PRO A 539 VAL A 543 5 5
HELIX 15 15 ASN A 557 HIS A 564 1 8
HELIX 16 16 TRP A 607 HIS A 622 1 16
HELIX 17 17 SER A 628 LYS A 639 1 12
HELIX 18 18 ALA A 640 LEU A 643 5 4
HELIX 19 19 ASP A 644 LEU A 672 1 29
HELIX 20 20 ASP A 681 LEU A 685 5 5
HELIX 21 21 PRO A 686 ARG A 690 5 5
HELIX 22 22 HIS A 718 LEU A 722 5 5
HELIX 23 23 PRO A 726 TYR A 728 5 3
HELIX 24 24 THR A 737 SER A 754 1 18
SHEET 1 AA 8 VAL A 34 PHE A 35 0
SHEET 2 AA 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35
SHEET 3 AA 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64
SHEET 4 AA 8 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581
SHEET 5 AA 8 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512
SHEET 6 AA 8 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599
SHEET 7 AA 8 THR A 422 ALA A 430 -1 O GLY A 426 N VAL A 489
SHEET 8 AA 8 ARG A 86 ARG A 89 -1 O ARG A 86 N TYR A 425
SHEET 1 AB 2 HIS A 82 PHE A 83 0
SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83
SHEET 1 AC 2 GLN A 96 THR A 97 0
SHEET 2 AC 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96
SHEET 1 AD 4 SER A 495 HIS A 499 0
SHEET 2 AD 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499
SHEET 3 AD 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590
SHEET 4 AD 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521
SHEET 1 AE 3 ASP A 676 ARG A 679 0
SHEET 2 AE 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676
SHEET 3 AE 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733
SSBOND 1 CYS A 706 CYS A 723 1555 1555 2.07
SSBOND 2 CYS A 708 CYS A 725 1555 1555 2.04
LINK O LEU A 413 MN MN A 801 1555 1555 2.72
LINK O THR A 416 MN MN A 801 1555 1555 2.67
LINK NE2 HIS A 499 MN MN A 802 1555 1555 2.21
LINK OE2 GLU A 501 MN MN A 802 1555 1555 2.19
LINK NE2 HIS A 587 MN MN A 802 1555 1555 2.22
LINK SG CYS A 692 ZN ZN A 800 1555 1555 2.15
LINK SG CYS A 695 ZN ZN A 800 1555 1555 2.40
LINK SG CYS A 715 ZN ZN A 800 1555 1555 2.24
LINK ND1 HIS A 718 ZN ZN A 800 1555 1555 2.08
LINK MN MN A 802 N2 QAY A 901 1555 1555 1.99
LINK MN MN A 802 N1 QAY A 901 1555 1555 2.78
LINK MN MN A 802 N5 QAY A 901 1555 1555 2.11
LINK MN MN A 802 O HOH A2141 1555 1555 2.01
SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718
SITE 1 AC2 6 LEU A 90 ASN A 91 LEU A 413 THR A 416
SITE 2 AC2 6 GLU A 419 HOH A2058
SITE 1 AC3 5 HIS A 499 GLU A 501 HIS A 587 QAY A 901
SITE 2 AC3 5 HOH A2141
SITE 1 AC4 11 TYR A 425 ASP A 428 TYR A 488 PHE A 496
SITE 2 AC4 11 HIS A 499 GLU A 501 LYS A 517 TRP A 519
SITE 3 AC4 11 HIS A 587 MN A 802 HOH A2141
SITE 1 AC5 6 ASP A 630 CYS A 699 PHE A 700 MET A 701
SITE 2 AC5 6 SER A 702 HOH A2206
SITE 1 AC6 3 GLY A 524 HOH A2155 HOH A2279
SITE 1 AC7 6 ILE A 500 TRP A 504 ARG A 584 HIS A 617
SITE 2 AC7 6 TYR A 618 LEU A 621
CRYST1 142.910 142.910 152.100 90.00 90.00 120.00 P 65 2 2 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006997 0.004040 0.000000 0.00000
SCALE2 0.000000 0.008080 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006575 0.00000